ZC4H2 loss of function is associated with temporal dysregulation of neural stem proliferation and neuron development

ZC4H2 is an X-linked zinc finger transcription factor essential for early neurodevelopment. Pathogenic variants in ZC4H2 are associated with both central and peripheral nervous system pathologies. The molecular and cellular mechanisms driving these phenotypes remain poorly understood, particularly in human female models that have undergone X chromosome inactivation. Neuronal models were differentiated from a human female cell line with a de novo Xq11.2 deletion causing ZC4H2 loss of function, associated with arthrogryposis multiplex congenita and cognitive impairment. Using iPSC-derived neural stem cells and cortical organoids, we identified premature neuronal differentiation, reduced BMP-SMAD signaling, and decreased SMAD1/5 phosphorylation. In cortical organoids, ZC4H2 deficiency altered neurogenesis timing, retaining proliferative progenitors while prematurely activating neuronal programs, leading to enlarged organoids with persistent dysregulation of gene programs required for complete neuronal maturation. We identified ZC4H2 target genes likely to mediate these phenotypes and tested a codon-optimized transgene showing both the restoration of SMAD1/5 phosphorylation, BMPR2 gene expression, and improved neuronal complexity. These results demonstrate effective ZC4H2 restoration in complex human models and highlight therapeutic potential for ZC4H2-linked neurodevelopmental disorders.